Fifa is investigating whether its transport and distribution systems had failed after empty seats were visible at World Cup venues for a second day running.

Patches of empty seats at the match between South Korea and Greece yesterday in Port Elizabeth were blamed on a breakdown in the transport system designed to get thousands of tickets distributed to local government, the South African Football Association and businesses to the matches.

There were 10,955 empty seats at a stadium with a usable capacity of 42,486. There were also large numbers of empty seats at today's match between Algeria and Slovenia in Polokwane, where the official attendance of 30,325 was well down on the World Cup capacity of 41,733. Earlier in the day, a Fifa spokesman said there were only 700 tickets left for the match, indicating that again many of those who had tickets were unable or unwilling to turn up.

The game between Serbia and Ghana at the 42,858-capacity Lotus Versfeld stadium in Pretoria was reported as a sell-out but the actual attendance was 38,833.

Fifa has had to work hard to shift tickets for the South African World Cup in the face of criticism over its pricing and hospitality sales strategies. But last week the governing body's secretary general, Jérôme Valcke, said the tickets were between 97% and 98% sold out.

The empty seats – which look terrible on television – are a problem for Fifa because, having sold batches of tickets at reduced prices to local groups, it cannot now put them back on the market.

A Fifa spokesman said a transport system to ferry the groups to the South Korea v Greece match and other less attractive fixtures did not appear to have worked properly. He said: "It looked like a lot of people did not show up at the stadium. We are investigating this. We asked for a system to be put in place. Apparently, that has not completely worked. We are working on this to make sure this is not the case for a potential few others of those games."

While Fifa insists those tickets account for the vast majority of the total, there are also suspicions that a number of tickets are still in the hands of third party agencies who overestimated international demand and are unable to shift them.

Fifa and the local organising committee have pointed out that unattractive early games in major tournaments are often not full and said they were happy with attendances overall. The average from the first five games of 54,887 would make the tournament the second best attended since 1982 if it could be maintained for the entire tournament.

Problems with empty seats for the opening ceremony at Soccer City were attributed to supporters' reluctance to put their faith in public transport, causing gridlock on approach roads as too many fans tried to get to the stadium by car. A spokesman for the organising committee urged fans to use the park and ride systems that have been set up to ferry them to stadiums: "Issues are being addressed but the onus is on supporters to arrive early and to use transport provided by the city."

Although empty seats were visible during England's match with the USA in Rustenburg, long claimed as sold out, Fifa said they were so-called "kill" seats that don't provide an acceptable view or are required by broadcasters. The Royal Bafokeng stadium has a total capacity of 45,000 but only 38,646 of those seats are usable during the World Cup.